@text "TERTIARY STRUCTURE -- THE FOUR HELIX BUNDLE (HEMERYTHRIN)" When 2 or more secondary structure elements group together, they form what is known as 'tertiary structure motifs'. This kinemage shows the arrangement of four separate helices to form a bundle. You can turn on the rest of the protein to see how the four helices are derived from different regions of one continuous amino acid chain (click on 'turns' and 'rest'). The amino acids which are not involved in forming helices take part in 'loops' and 'turns'. Turn on the sidechains to see which point in toward the middle of the bundle to form the hydrophobic core. This type of motif can be found in a number of different proteins; here you are looking at hemerythrin (from PDB file, 1HMO). Hemerythrin is a protein which functions in marine invertebrates (like mollusks) the way hemoglobin functions in humans: it binds oxygen and then transports it to where the organism needs it. In this kinemage, you can highlight the region within the bundle where one oxygen molecule binds (2 atoms of oxygen per oxygen molecule; red). Specifically, iron atoms (Fe; blue) held in place by sidechains of the protein, in turn bind to the oxygen (hemoglobin also uses iron for this purpose. Remember that iron-deficiencies lead to anemia, i.e., not enough oxygen can get to the parts of your body that need it). @kinemage 1 @caption Calpha trace of the four-helix bundle of hemerythrin (seagreen). Note their antiparallel arrangement. Turn on 'turns' (skyblue) & 'rest' (pinktint) to see the turns connecting pairs of helices, as well as the remainder of the protein. Click on 'helices' & 'other' under 'Sidechains' to add the helical (gold) & other (yellowtint) residues to the display. Select view2 for a look through the center of the bundle. Turn on 'Fe/oxygen' (blue/red) to see the active site of the protein; view3 is a close-up of this region. @onewidth @viewid {Side} @zoom 1.00 @zslab 200 @center -2.249 22.705 15.622 @matrix -0.104083 -0.911180 -0.398647 -0.592851 0.378669 -0.710730 0.798558 0.162363 -0.579607 @2viewid {Top} @2zoom 1.12 @2zslab 180 @2center -2.249 22.705 15.622 @2matrix -0.17225 0.51436 -0.84010 -0.59292 0.62691 0.50540 0.78662 0.58517 0.19699 @3viewid {Close-up} @3zoom 2.60 @3zslab 290 @3center 2.514 21.203 16.350 @3matrix -0.127396 -0.909862 -0.394870 -0.675859 0.371013 -0.636839 0.725937 0.185745 -0.662204 @group {4-HLX BUND} @subgroup {Alpha-C's} @vectorlist {helices} color=seagreen {ca thr a 19}P 5.686 18.622 3.779 {ca ile a 20}3.09 16.579 5.638 {ca ile a 21}3.583 18.704 8.758 {ca asp a 22}3.415 21.961 6.791 {ca asp a 23}0.146 20.895 5.021 {ca glu a 24}-1.389 20.089 8.388 {ca his a 25}-0.298 23.411 9.852 {ca lys a 26}-2.119 25.191 7.039 {ca thr a 27}-5.291 23.543 8.272 {ca leu a 28}-4.731 24.913 11.784 {ca phe a 29}-4.325 28.499 10.517 {ca asn a 30}-7.556 28.11 8.526 {ca gly a 31}-9.427 26.754 11.581 {ca ile a 32}-8.417 29.806 13.686 {ca leu a 33}-9.273 32.156 10.817 {ca leu a 34}-12.811 30.703 10.529 {ca leu a 35}-13.363 31.158 14.265 {ca ser a 36}-12.228 34.821 13.933 {ca his a 43}P -15.819 26.336 13.019 {ca leu a 44}-14.726 25.009 16.368 {ca asn a 45}-15.36 21.389 15.258 {ca glu a 46}-13.237 21.927 12.202 {ca leu a 47}-10.356 23.38 14.164 {ca arg a 48}-10.702 20.785 16.943 {ca arg a 49}-10.666 17.884 14.434 {ca cys a 50}-7.631 19.245 12.547 {ca thr a 51}-5.754 19.964 15.746 {ca gly a 52}-6.349 16.559 17.35 {ca lys a 53}-5.259 14.907 14.134 {ca his a 54}-2.193 17.084 13.582 {ca phe a 55}-1.029 16.716 17.192 {ca leu a 56}-1.28 12.93 17.012 {ca asn a 57}0.46 12.677 13.63 {ca glu a 58}3.289 14.94 14.715 {ca gln a 59}3.602 12.942 17.917 {ca gln a 60}3.903 9.793 15.863 {ca leu a 61}6.625 11.329 13.727 {ca met a 62}8.533 12.258 16.92 {ca gln a 63}8.162 8.708 18.263 {ca gly a 69}P 11.829 16.251 23.295 {ca tyr a 70}8.66 14.196 22.921 {ca ala a 71}7.282 14.359 26.438 {ca glu a 72}7.514 18.086 26.739 {ca his a 73}6.119 18.55 23.25 {ca lys a 74}3.179 16.251 23.902 {ca lys a 75}2.354 18.162 27.078 {ca ala a 76}2.19 21.455 25.141 {ca his a 77}-0.191 19.93 22.566 {ca asp a 78}-2.398 18.479 25.265 {ca asp a 79}-2.65 21.854 27.035 {ca phe a 80}-3.925 23.399 23.811 {ca ile a 81}-6.51 20.627 23.216 {ca his a 82}-7.731 21.346 26.727 {ca lys a 83}-8.19 24.979 25.728 {ca leu a 84}-10.133 23.936 22.65 {ca asp a 85}-12.284 21.587 24.749 {ca thr a 92}P -6.429 36.17 20.303 {ca tyr a 93}-4.965 33.563 22.548 {ca ala a 94}-5.293 30.954 19.825 {ca lys a 95}-3.676 33.123 17.132 {ca asn a 96}-0.71 33.766 19.335 {ca trp a 97}-0.512 30.201 20.639 {ca leu a 98}-0.206 28.676 17.186 {ca val a 99}2.398 31.103 15.785 {ca asn a 100}4.555 30.685 18.87 {ca his a 101}4.181 26.915 18.982 {ca ile a 102}5.326 26.343 15.469 {ca lys a 103}8.177 28.879 15.51 {ca thr a 104}9.634 27.795 18.858 {ca ile a 105}8.433 24.194 19.757 {ca asp a 106}7.97 22.554 16.367 {ca phe a 107}11.047 24.296 14.96 {ca lys a 108}13.118 22.489 17.576 @vectorlist {turns} off color=skyblue {ca ser a 36}P -12.228 34.821 13.933 {ca gln a 37}-14.914 35.245 11.225 {ca ala a 38}-17.617 33.483 13.301 {ca asp a 39}-17.219 31.84 16.69 {ca asn a 40}-19.634 28.936 16.185 {ca ala a 41}-19.837 25.146 16.567 {ca asp a 42}-18.981 24.253 12.961 {ca his a 43}-15.819 26.336 13.019 {ca gln a 63}P 8.162 8.708 18.263 {ca ser a 64}9.48 7.136 15.064 {ca ser a 65}12.949 8.505 15.764 {ca gln a 66}12.586 8.326 19.56 {ca tyr a 67}12.806 12.149 19.711 {ca ala a 68}14.228 13.266 23.033 {ca gly a 69}11.829 16.251 23.295 {ca asp a 85}P -12.284 21.587 24.749 {ca thr a 86}-13.116 24.355 27.258 {ca trp a 87}-13.349 27.029 24.524 {ca asp a 88}-14.03 30.51 25.871 {ca gly a 89}-13.939 32.348 22.506 {ca asp a 90}-10.478 33.864 23.064 {ca val a 91}-9.378 33.934 19.427 {ca thr a 92}-6.429 36.17 20.303 @vectorlist {rest} off color=pinktint {ca gly a 1}P 7.168 37.69 19.95 {ca gly a 1}7.168 37.69 19.95 {ca phe a 2}6.635 36.645 16.355 {ca pro a 3}4.392 38.702 14.149 {ca ile a 4}0.787 37.503 13.797 {ca pro a 5}-0.097 37.086 10.109 {ca asp a 6}-2.939 39.185 8.813 {ca pro a 7}-4.894 37.749 7.253 {ca tyr a 8}-4.35 34.836 9.631 {ca cys a 9}-2.953 32.364 7.107 {ca trp a 10}0.14 30.174 6.869 {ca asp a 11}3.152 31.674 5.078 {ca ile a 12}6.484 30.111 4.101 {ca ser a 13}8.159 31.645 7.192 {ca phe a 14}6.409 28.767 9.033 {ca arg a 15}8.072 26.088 6.95 {ca thr a 16}9.345 23.063 8.836 {ca phe a 17}10.602 21.223 5.696 {ca tyr a 18}8.335 18.27 6.494 {ca thr a 19}5.686 18.622 3.779 {ca lys a 108}P 13.118 22.489 17.576 {ca tyr a 109}12.466 19.019 16.123 {ca arg a 110}13.806 19.98 12.646 {ca gly a 111}16.685 17.707 11.66 {ca lys a 112}15.917 15.313 14.543 {ca ile a 113}12.887 13.453 13.247 @subgroup {Fe/oxygen} dominant off @balllist {iron} radius=.3 color=blue {Fe}P 4.165 20.657 17.319 {Fe}P 3.297 21.33 14.316 @balllist {oxygen} radius=.2 color=red {O}P 1.513 22.914 15.015 {O}P 2.667 21.163 16.305 @vectorlist {Fe-O bonds} color=blue {O} P U 2.667, 21.163, 16.305 {Fe} L U 4.165, 20.657, 17.319 {O} P U 2.667, 21.163, 16.305 {Fe} L U 3.297, 21.330, 14.316 @vectorlist {O-O bonds} color=red {O} P U 2.667, 21.163, 16.305 {O} L U 1.513, 22.914, 15.015 @subgroup {Sidechains} @vectorlist {helices} off color= gold {ca thr a 19}P 5.686 18.622 3.779 {cb thr a 19}5.827 18.168 2.264 {og1 thr a 19}5.733 16.74 2.23 {cb thr a 19}P 5.827 18.168 2.264 {cg2 thr a 19}7.123 18.719 1.668 {ca ile a 20}P 3.09 16.579 5.638 {cb ile a 20}3.203 15.038 5.962 {cg1 ile a 20}1.864 14.507 6.44 {cd1 ile a 20}1.542 14.321 7.957 {cb ile a 20}P 3.203 15.038 5.962 {cg2 ile a 20}4.38 14.783 6.969 {ca ile a 21}P 3.583 18.704 8.758 {cb ile a 21}4.918 18.775 9.57 {cg1 ile a 21}5.225 17.389 10.136 {cd1 ile a 21}4.918 17.019 11.544 {cb ile a 21}P 4.918 18.775 9.57 {cg2 ile a 21}4.865 19.92 10.624 {ca asp a 22}P 3.415 21.961 6.791 {cb asp a 22}4.375 22.468 5.688 {cg asp a 22}5.78 22.789 6.207 {od1 asp a 22}6.002 22.956 7.434 {cg asp a 22}P 5.78 22.789 6.207 {od2 asp a 22}6.668 22.778 5.338 {ca asp a 23}P 0.146 20.895 5.021 {cb asp a 23}0.032 19.761 4.015 {cg asp a 23}0.722 20.066 2.731 {od1 asp a 23}0.892 19.187 1.88 {cg asp a 23}P 0.722 20.066 2.731 {od2 asp a 23}1.077 21.253 2.485 {ca glu a 24}P -1.389 20.089 8.388 {cb glu a 24}-0.918 19.032 9.433 {cg glu a 24}-1.11 17.599 8.946 {cd glu a 24}-0.771 16.441 9.83 {oe1 glu a 24}-1.168 15.316 9.507 {cd glu a 24}P -0.771 16.441 9.83 {oe2 glu a 24}-0.104 16.687 10.849 {ca his a 25}P -0.298 23.411 9.852 {cb his a 25}1.116 24.01 9.959 {cg his a 25}1.946 23.333 11.022 {nd1 his a 25}3.335 23.373 11.012 {ce1 his a 25}3.747 22.775 12.113 {ne2 his a 25}2.747 22.233 12.784 {ne2 his a 25}P 2.747 22.233 12.784 {ce1 his a 25}3.747 22.775 12.113 {cg his a 25}P 1.946 23.333 11.022 {cd2 his a 25}1.606 22.591 12.09 {ne2 his a 25}2.747 22.233 12.784 {ce1 his a 25}3.747 22.775 12.113 {ca lys a 26}P -2.119 25.191 7.039 {cb lys a 26}-1.94 24.86 5.576 {cg lys a 26}-0.605 25.31 4.986 {cd lys a 26}-0.391 24.738 3.598 {ce lys a 26}1.1 24.792 3.246 {nz lys a 26}1.383 24.079 2.022 {ca thr a 27}P -5.291 23.543 8.272 {cb thr a 27}-5.722 22.02 8.255 {og1 thr a 27}-5.091 21.333 9.408 {cb thr a 27}P -5.722 22.02 8.255 {cg2 thr a 27}-5.386 21.292 6.97 {ca leu a 28}P -4.731 24.913 11.784 {cb leu a 28}-3.679 24.47 12.746 {cg leu a 28}-3.378 22.997 12.94 {cd1 leu a 28}-2.535 22.879 14.226 {cg leu a 28}P -3.378 22.997 12.94 {cd2 leu a 28}-4.624 22.209 13.145 {ca phe a 29}P -4.325 28.499 10.517 {cb phe a 29}-3.29 28.99 9.497 {cg phe a 29}-1.954 29.299 10.124 {cd1 phe a 29}-0.993 28.295 10.248 {ce1 phe a 29}0.269 28.615 10.763 {cz phe a 29}0.484 29.907 11.235 {cg phe a 29}P -1.954 29.299 10.124 {cd2 phe a 29}-1.696 30.611 10.55 {ce2 phe a 29}-0.481 30.935 11.156 {cz phe a 29}0.484 29.907 11.235 {ca asn a 30}P -7.556 28.11 8.526 {cb asn a 30}-7.772 27.123 7.37 {cg asn a 30}-9.189 27.192 6.794 {od1 asn a 30}-9.48 28.114 6.025 {cg asn a 30}P -9.189 27.192 6.794 {nd2 asn a 30}-10.074 26.325 7.294 {ca ile a 32}P -8.417 29.806 13.686 {cb ile a 32}-7.019 30.099 14.302 {cg1 ile a 32}-6.675 28.934 15.264 {cd1 ile a 32}-5.21 28.977 15.819 {cb ile a 32}P -7.019 30.099 14.302 {cg2 ile a 32}-6.963 31.439 15.049 {ca leu a 33}P -9.273 32.156 10.817 {cb leu a 33}-8.632 32.122 9.428 {cg leu a 33}-9.28 33.126 8.439 {cd1 leu a 33}-8.495 34.433 8.472 {cg leu a 33}P -9.28 33.126 8.439 {cd2 leu a 33}-9.276 32.534 7.072 {ca leu a 34}P -12.811 30.703 10.529 {cb leu a 34}-13.179 29.269 10.155 {cg leu a 34}-12.772 28.725 8.814 {cd1 leu a 34}-13.21 27.255 8.694 {cg leu a 34}P -12.772 28.725 8.814 {cd2 leu a 34}-13.391 29.521 7.696 {ca leu a 35}P -13.363 31.158 14.265 {cb leu a 35}-12.66 30.524 15.435 {cg leu a 35}-12.934 29.083 15.777 {cd1 leu a 35}-11.974 28.64 16.886 {cg leu a 35}P -12.934 29.083 15.777 {cd2 leu a 35}-14.362 28.906 16.259 {ca ser a 36}P -12.228 34.821 13.933 {cb ser a 36}-10.852 35.375 13.594 {og ser a 36}-10.701 35.37 12.149 {ca his a 43}P -15.819 26.336 13.019 {cb his a 43}-15.79 27.88 13.127 {cg his a 43}-16.33 28.528 11.894 {nd1 his a 43}-16.549 29.891 11.8 {ce1 his a 43}-16.993 30.179 10.597 {ne2 his a 43}-17.11 29.077 9.898 {ne2 his a 43}P -17.11 29.077 9.898 {ce1 his a 43}-16.993 30.179 10.597 {cg his a 43}P -16.33 28.528 11.894 {cd2 his a 43}-16.695 28.053 10.693 {ne2 his a 43}-17.11 29.077 9.898 {ce1 his a 43}-16.993 30.179 10.597 {ca leu a 44}P -14.726 25.009 16.368 {cb leu a 44}-15.314 25.265 17.733 {cg leu a 44}-14.568 24.66 18.923 {cd1 leu a 44}-13.192 25.326 19.044 {cg leu a 44}P -14.568 24.66 18.923 {cd2 leu a 44}-15.396 24.88 20.159 {ca asn a 45}P -15.36 21.389 15.258 {cb asn a 45}-16.679 20.865 14.679 {cg asn a 45}-17.737 20.593 15.709 {od1 asn a 45}-18.901 20.339 15.297 {cg asn a 45}P -17.737 20.593 15.709 {nd2 asn a 45}-17.473 20.617 16.99 {ca glu a 46}P -13.237 21.927 12.202 {cb glu a 46}-13.498 23.009 11.161 {cg glu a 46}-13.029 22.749 9.753 {cd glu a 46}-13.432 21.533 9.012 {oe1 glu a 46}-12.751 20.984 8.162 {cd glu a 46}P -13.432 21.533 9.012 {oe2 glu a 46}-14.611 21.141 9.248 {ca leu a 47}P -10.356 23.38 14.164 {cb leu a 47}-10.346 24.742 14.887 {cg leu a 47}-9.084 25.035 15.723 {cd1 leu a 47}-7.867 25.095 14.803 {cg leu a 47}P -9.084 25.035 15.723 {cd2 leu a 47}-9.245 26.343 16.481 {ca arg a 48}P -10.702 20.785 16.943 {cb arg a 48}-11.86 20.569 17.879 {cg arg a 48}-11.718 19.437 18.901 {cd arg a 48}-10.539 19.664 19.806 {ne arg a 48}-10.56 18.763 20.928 {cz arg a 48}-10.215 17.479 20.901 {nh1 arg a 48}-10.242 16.705 21.974 {cz arg a 48}P -10.215 17.479 20.901 {nh2 arg a 48}-9.721 16.975 19.737 {ca arg a 49}P -10.666 17.884 14.434 {cb arg a 49}-11.653 17.557 13.332 {cg arg a 49}-11.368 16.362 12.449 {cd arg a 49}-12.235 16.263 11.261 {ne arg a 49}-12.155 17.299 10.247 {cz arg a 49}-11.176 17.479 9.362 {nh1 arg a 49}-11.207 18.428 8.408 {cz arg a 49}P -11.176 17.479 9.362 {nh2 arg a 49}-10.078 16.714 9.432 {ca cys a 50}P -7.631 19.245 12.547 {cb cys a 50}-7.667 20.5 11.674 {sg cys a 50}-8.663 20.25 10.24 {ca thr a 51}P -5.754 19.964 15.746 {cb thr a 51}-6.233 20.999 16.839 {og1 thr a 51}-6.399 22.283 16.124 {cb thr a 51}P -6.233 20.999 16.839 {cg2 thr a 51}-5.27 21.149 18.018 {ca lys a 53}P -5.259 14.907 14.134 {cb lys a 53}-5.974 15.039 12.809 {cg lys a 53}-5.378 14.291 11.615 {cd lys a 53}-6.203 14.696 10.348 {ce lys a 53}-5.338 15.443 9.38 {nz alys a 53}-5.851 16.739 8.906 {ce lys a 53}P -5.338 15.443 9.38 {nz blys a 53}-4.77 14.533 8.344 {ca his a 54}P -2.193 17.084 13.582 {cb his a 54}-2.111 18.597 13.324 {cg his a 54}-0.69 19.084 13.36 {nd1 his a 54}0.258 18.631 12.504 {ce1 his a 54}1.43 19.166 12.852 {ne2 his a 54}1.233 19.964 13.881 {ne2 his a 54}P 1.233 19.964 13.881 {ce1 his a 54}1.43 19.166 12.852 {cg his a 54}P -0.69 19.084 13.36 {cd2 his a 54}-0.069 19.912 14.235 {ne2 his a 54}1.233 19.964 13.881 {ce1 his a 54}1.43 19.166 12.852 {ca phe a 55}P -1.029 16.716 17.192 {cb phe a 55}-1.74 17.258 18.43 {cg phe a 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14.055 19.838 {cd gln a 59}1.12 14.131 20.606 {oe1 gln a 59}0.526 13.1 20.985 {cd gln a 59}P 1.12 14.131 20.606 {ne2 gln a 59}0.656 15.307 20.946 {ca gln a 60}P 3.903 9.793 15.863 {cb gln a 60}2.831 9.161 14.91 {cg gln a 60}1.708 8.724 15.85 {cd gln a 60}0.597 7.92 15.292 {oe1 gln a 60}-0.127 7.261 16.082 {cd gln a 60}P 0.597 7.92 15.292 {ne2 gln a 60}0.363 7.964 13.975 {ca leu a 61}P 6.625 11.329 13.727 {cb leu a 61}6.367 12.561 12.844 {cg leu a 61}7.49 12.996 11.914 {cd1 leu a 61}7.944 11.888 10.974 {cg leu a 61}P 7.49 12.996 11.914 {cd2 leu a 61}6.961 14.178 11.096 {ca met a 62}P 8.533 12.258 16.92 {cb met a 62}8.069 13.192 18.051 {cg met a 62}8.052 14.646 17.548 {sd met a 62}7.434 15.691 18.917 {ce met a 62}5.751 15.906 18.594 {ca gln a 63}P 8.162 8.708 18.263 {cb gln a 63}6.819 8.011 18.583 {cg gln a 63}6.319 8.394 19.943 {cd gln a 63}4.987 7.752 20.271 {oe1 gln a 63}3.968 7.974 19.605 {cd gln a 63}P 4.987 7.752 20.271 {ne2 gln a 63}5.025 6.936 21.307 {ca tyr a 70}P 8.66 14.196 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asp a 90}P -8.575 34.787 24.499 {od2 asp a 90}-8.309 35.537 23.541 {ca val a 91}P -9.378 33.934 19.427 {cb val a 91}-10.259 34.547 18.333 {cg1 val a 91}-9.606 34.613 16.962 {cb val a 91}P -10.259 34.547 18.333 {cg2 val a 91}-11.571 33.797 18.21 {ca tyr a 109}P 12.466 19.019 16.123 {cb tyr a 109}11.182 18.143 16.186 {cg tyr a 109}9.998 18.607 15.392 {cd1 tyr a 109}10.034 18.801 14.022 {ce1 tyr a 109}8.939 19.205 13.295 {cz tyr a 109}7.708 19.34 13.991 {oh tyr a 109}6.615 19.736 13.28 {cg tyr a 109}P 9.998 18.607 15.392 {cd2 tyr a 109}8.751 18.756 16.049 {ce2 tyr a 109}7.629 19.151 15.342 {cz tyr a 109}7.708 19.34 13.991 {ca arg a 110}P 13.806 19.98 12.646 {cb arg a 110}13.783 21.355 11.967 {cg arg a 110}12.399 22.018 11.991 {cd arg a 110}12.403 23.195 11.014 {ne arg a 110}13.101 24.274 11.648 {cz arg a 110}13.322 25.492 11.176 {nh1 arg a 110}12.884 25.922 10.018 {cz arg a 110}P 13.322 25.492 11.176 {nh2 arg a 110}14.117 26.233 11.967 {ca lys a 112}P 15.917 15.313 14.543 {cb lys a 112}15.734 15.904 15.964 {cg lys a 112}16.798 16.953 16.254 {cd lys a 112}16.608 17.609 17.598 {ce lys a 112}17.433 18.882 17.72 {nz lys a 112}16.87 19.722 18.831 {ca ile a 113}P 12.887 13.453 13.247 {cb ile a 113}11.579 13.825 14.019 {cg1 ile a 113}10.89 15.06 13.388 {cd1 ile a 113}9.525 15.469 13.984 {cb ile a 113}P 11.579 13.825 14.019 {cg2 ile a 113}11.83 14.035 15.54